[2026-05-28T21:13:43] Launching Arriba 2.4.0
[2026-05-28T21:13:43] Loading assembly from 'ref_genome.fa' 
[2026-05-28T21:13:56] Loading annotation from 'ref_annot.gtf' 
[2026-05-28T21:14:00] Reading chimeric alignments from 'RT4_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam' (total=13072331)
[2026-05-28T21:23:34] Marking multi-mapping alignments (marked=9029283)
[2026-05-28T21:23:40] Detecting strandedness (reverse)
[2026-05-28T21:23:40] Assigning strands to alignments 
[2026-05-28T21:23:43] Annotating alignments 
[2026-05-28T21:24:32] Filtering duplicates (remaining=8986097)
[2026-05-28T21:24:43] Filtering mates which do not map to interesting contigs (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y AC_* NC_*) (remaining=8266052)
[2026-05-28T21:24:45] Filtering mates which only map to viral contigs (AC_* NC_*) (remaining=8266052)
[2026-05-28T21:24:48] Filtering viral contigs with expression lower than the top 5 (remaining=8266052)
[2026-05-28T21:24:54] Filtering viral contigs with less than 5% coverage (remaining=8266052)
[2026-05-28T21:24:57] Estimating fragment length (mate gap mean=-83.9896, mate gap stddev=30.5246, read length mean=127.324)
[2026-05-28T21:24:58] Filtering read-through fragments with a distance <=10000bp (remaining=7908028)
[2026-05-28T21:25:01] Filtering inconsistently clipped mates (remaining=7770422)
[2026-05-28T21:25:04] Filtering breakpoints adjacent to homopolymers >=6nt (remaining=7448502)
[2026-05-28T21:25:10] Filtering fragments with small insert size (remaining=7447030)
[2026-05-28T21:25:13] Filtering alignments with long gaps (remaining=7447030)
[2026-05-28T21:25:16] Filtering fragments with both mates in the same gene (remaining=7445359)
[2026-05-28T21:25:19] Filtering fusions arising from hairpin structures (remaining=6970416)
[2026-05-28T21:25:23] Filtering reads with a mismatch p-value <=0.01 (remaining=3148349)
[2026-05-28T21:25:43] Filtering reads with low entropy (k-mer content >=60%) (remaining=1251443)
[2026-05-28T21:25:58] Finding fusions and counting supporting reads (total=999513)
[2026-05-28T21:26:23] Merging adjacent fusion breakpoints (remaining=992131)
[2026-05-28T21:26:25] Filtering multi-mapping fusions by alignment score and read support (remaining=596331)
[2026-05-28T21:27:07] Estimating expected number of fusions by random chance (e-value) 
[2026-05-28T21:27:18] Filtering fusions with both breakpoints in adjacent non-coding/intergenic regions (remaining=593367)
[2026-05-28T21:27:19] Filtering intragenic fusions with both breakpoints in exonic regions (remaining=375549)
[2026-05-28T21:27:20] Filtering fusions with <2 supporting reads (remaining=34612)
[2026-05-28T21:27:21] Filtering fusions with an e-value >=0.3 (remaining=8319)
[2026-05-28T21:27:22] Searching for internal tandem duplications <=100bp with >=10 supporting reads and >=7% allele fraction (remaining=8370)
[2026-05-28T21:27:27] Filtering fusions with both breakpoints in intronic/intergenic regions (remaining=8190)
[2026-05-28T21:27:28] Searching for known fusions in 'known_fusions_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=8241)
[2026-05-28T21:27:30] Filtering in vitro-generated fusions between genes with an expression above the 99.8% quantile (remaining=6421)
[2026-05-28T21:27:37] Searching for fusions with spliced split reads (remaining=6434)
[2026-05-28T21:27:45] Selecting best breakpoints from genes with multiple breakpoints (remaining=4120)
[2026-05-28T21:27:47] Filtering read-through fusions with breakpoints near the gene boundary (remaining=4087)
[2026-05-28T21:27:48] Searching for fusions with >=4 spliced events (remaining=5190)
[2026-05-28T21:27:50] Filtering blacklisted fusions in 'blacklist_hg38_GRCh38_v2.4.0.tsv.gz' (remaining=2276)
[2026-05-28T21:28:20] Filtering fusions with anchors <=23nt (remaining=1793)
[2026-05-28T21:28:21] Filtering end-to-end fusions with low support (remaining=1754)
[2026-05-28T21:28:22] Filtering fusions with no coverage around the breakpoints (remaining=1730)
[2026-05-28T21:28:24] Indexing gene sequences 
[2026-05-28T21:28:33] Filtering genes with >=30% identity (remaining=486)
[2026-05-28T21:28:37] Re-aligning chimeric reads to filter fusions with >=80% mis-mappers (remaining=200)
[2026-05-28T21:28:42] Selecting best breakpoints from genes with multiple breakpoints (remaining=128)
[2026-05-28T21:28:44] Searching for additional isoforms (remaining=193)
[2026-05-28T21:28:46] Assigning confidence scores to events 
[2026-05-28T21:28:53] Loading protein domains from 'protein_domains_hg38_GRCh38_v2.4.0.gff3'
[2026-05-28T21:28:53] Writing fusions to file 'RT4_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.tsv' 
[2026-05-28T21:28:56] Writing discarded fusions to file 'RT4_FFPE_RNA_0001_B23LG7FLT4_3.arriba.fusions.discarded.tsv'
[2026-05-28T21:29:46] Freeing resources
[2026-05-28T21:30:13] Done (elapsed time=00:16:30, CPU time=00:16:29, peak memory=18.1gb)